Study summary: The present study was designed to evaluate the effects of diets containing mainly casein, soy protein isolate, or whey as protein sources by means of short-term, long-term, and multigenerational studies in rats. Soy protein isolate, casein and whey all are used as the major proteins in the infant formulas sold in the U.S. Concerns have developed over soy-based infant formula, in part because of the potential impact of phytoestrogens during important periods of infant development. The current study found only minor differences in body weight gain profiles in the casein-, soy protein isolate- and whey-fed rats and the three groups of rats did not differ in development, organ weights, hepatic metabolism of testosterone, or reproductive performance. However, some endocrine-related processes varied between the rats fed different diets. The soy protein isolate diet was found to accelerated puberty in female rats ( p <.05), whereas whey delayed puberty in both males and females, compared to casein ( p <.05). Male rats fed soy protein isolate were found to have normal serum testosterone levels, but female rats fed the same diet had reduced serum 17 β-estradiol concentrations and a blunted 17 β-estradiol response to ovariectomy, compared to rats fed casein or whey (p <.05). Female rats fed soy protein isolate or whey or treated with genistein were found to have reduced incidence of carcinogen-induced mammary tumors ( p <.05) compared to casein fed rats. Whey reduced tumor incidence by as much as 50%. The findings suggest certain gender-specific differences in development and endocrine responses among rats fed diets containing a single protein source. Whether similar effects occur in human infants fed single-source protein formula is unknown, however no such effects have been reported U.S. infants fed formula containing these proteins. The authors conclude that the long-term health consequence implications of early diet exposure to soy protein isolate and whey, such as reduced breast cancer incidence, are likely to be very positive.